I'm using Inkscape 0.48.5 r10040 so this might have already been addressed but I could not find anything on it.
What I am doing is putting an often used graphic object as a definition object in the <defs> section. I can use a reflink to it to make copies with minimum impact on file size.
What happens is that the size information of the definition object differs from what it really is. (It can be smaller or bigger.)
I have ruled out scaling errors, stroke errors, positioning/placement errors so the only conclusion is that the size information is wrong.
I have created a composed frame object to illustrate this. The error is about 1 pixel so it's not that visible compared to the original but you can see the mismatch with the other non-definition frame objects. See level name for reference description.
When I group it up the real overall size shows the discrepancy size correctly.
The problem can be easily adjusted for simple objects but complex ones can only be fixed with scaling. Nonetheless the problems is still there and will come up whenever you want to recreate it. Since it happens with any definition object it seems to be a bug but I'm not that sure.